R: Extract Meta-Communities

cutDendrogramAt {linkcomm} | R Documentation

## Extract Meta-Communities

### Description

This function extracts meta-communities from a dendrogram of community relatedness based on a user-defined place at which to cut the dendrogram.

### Usage

    cutDendrogramAt(x, lc = NULL, cutat = NULL, plot = TRUE, col = TRUE,
                    pal = brewer.pal(9, "Set1"), labels = FALSE, plotcut = TRUE,
                    right = TRUE, verbose = TRUE, ...)

### Arguments

`x` | An object of class `hclust`, usually generated by `getClusterRelatedness`.
`lc` | An object of class `linkcomm`. If included, the resulting plot will display additional information about the clusters. Defaults to NULL.
`cutat` | A numerical value at which to cut the dendrogram.
`plot` | Logical, whether to plot the dendrogram and the meta-communities, defaults to TRUE.
`col` | Logical, whether to colour the meta-communites.
`pal` | A character vector describing a colour palette to be used for colouring the meta-communites in the dendrogram plot. Defaults to `brewer.pal(9, "Set1")`.
`labels` | Logical, whether to put labels on the dendrogram. Defaults to FALSE.
`plotcut` | Logical, whether to display a horizontal line where the dendrogram is cut. Defaults to TRUE.
`right` | Logical, whether to orient the dendrogram to the right. Defaults to TRUE.
`verbose` | Logical, whether to display the progress of colouring the dendrogram. Defaults to TRUE.
`...` | Additional arguments to be passed to `plot`.

### Details

Extracting meta-communities allows the user to explore community relatedness and structure at higher levels.

### Value

A list of integer vectors, referring to meta-communities of link communities.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

### See Also

`getClusterRelatedness`

### Examples

    ## Generate graph, extract link communities, and cluster communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)
    hc <- getClusterRelatedness(lc)

    ## Cut dendrogram at 1 and extract meta-communities.
    cutDendrogramAt(hc, cutat = 1)

[Package linkcomm version 1.0-14 Index]